RE: [PyMOL] Can't load maps anymore!

mmand will draw a box around the map, showing you how it doesn't cover the PDB file. Either you need a model which covers the map, or a map which covers the model. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650

RE: [PyMOL] A couple of movie questions

> First up: Is there any way to tell PyMol *not* to change its view when > loading a > PDB file set auto_zoom,0 > Secondly: Below is an example of a small hack I have written when making > one > particular movie. This one overlays two molecules related by a 2-fold > axis by > doing a simple rota

RE: [PyMOL] negative images

ailing list), a copy of the problematic PNG file. Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mai

RE: [PyMOL] modifying atom coordinates

unpickling them in a Python interpreter. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol

RE: [PyMOL] alternative method for loading coordinates

sion of PyMOL, since _cmd isn't meant to be called by anyone except PyMOL. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-us

RE: [PyMOL] pymol raytracing crash

Thomas, I tried running your script on the current development version and on a version 0.90 binary, and wasn't able to get PyMOL to crash. How is PyMOL installed on your system? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Prin

RE: [PyMOL] Transparent cartoons?

visual artifacts will occur with standard OpenGL rendering. If you're on a PC, then you'll need to wait for the next big release, which will probably happen next week. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific

RE: [PyMOL] alternative method for loading coordinates

tely understand your question. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- >

RE: [PyMOL] pymol problems with Mandrake 9.1

rs, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of

RE: [PyMOL] incorporation of unusual amino acids

Uwe, > We plan a research project where we want to stepwise incorporate D-amino > acids into a peptide. To determine the exchanges it would be very useful > if > PyMol could assist. > If I might dream I would like to have D-amino acids (and maybe other un- > usual amino acids) available in the mut

RE: [PyMOL] individual surfaces?

-- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Dirk

RE: [PyMOL] How do I auto-load my startup pymol script in the new os x version?

/local/bin, or $HOME/bin By the way, this version of PyMOL can also work well on the mac as a PDB helper application with Netscape or IE. (For IE, type=TEXT creator=PyML) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] "Filled" view for deoxyribose rings, bases in DNA ???

Raji, Sorry, PyMOL can't do that yet. However, since you are probably the 10th person to ask for this, so it has become high priority for a future version... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC

RE: [PyMOL] adding a new external GUI

r own menu, which then creates it's own window in response to user requests. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From

[PyMOL] PyMOL for Mac G5, with Demos

o account. I'm no Mac-addict, but I do like to recognize and celebrate a good product when I see one. The dual 2 Ghz G5 running Mac OS X is a "killer" desktop computer for research -- Apple's first in a long time, and hopefully more will come if we appropriately reward this one with our business. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC

RE: [PyMOL] Python commands and variables

Yes, but you need to write in Python directly. For example: from pymol import cmd cmd.select("mysel","none") for i in range(10,20): cmd.select("mysel","mysel or resi %d"%i) Would work in a ".py" file. Cheers, Warren -- mailto:war...@dela

[PyMOL] Auto-launching in Mac Terminal

> I have a Mac TI powerbook running OSX. Every time I launch a new > terminal window, pymol launches. For example, if I open 3 terminal > windows, 3 pymol sessions also start. How do I stop this? What? You don't want PyMOL to launch every possible opportunity? Actually, I've encountered this

RE: [PyMOL] Re: cannot find _cmd module

roach. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourc

RE: [PyMOL] linker errors on win32?

Tina, "layer0/MemoryCache.c" is missing from the list of sources in the setup.py file. If you add that in right after the "layer0/MemoryDebug.c", it should build. Sorry about that! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Princi

RE: [PyMOL] Pymol & 3D printing

Thanks for your code! > P.S. I wish this mailing list had archives ... But it does! http://sourceforge.net/mailarchive/forum.php?forum_id=60 You can search by keyword. Look for the text box upper-left. Cheers, Warren

[PyMOL] RE: E-mail worm is going around

Jan, Thanks for that -- copy hereby sent to the PyMOL list. This is a relief. I was wondering why strange bounced email was coming back and had become concerned that infection had occurred here despite every precaution. SMTP-based email is indeed a hopeless cause. I vote fo

RE: [PyMOL] Different symmetry positions

mes differ slightly. Are you finding otherwise? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [ma

RE: [PyMOL] Delete Bonds

Jose, Select the bond using Ctrl-right-click, then either "unbond pk1,pk2" or hit Ctrl-D. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Ori

RE: [PyMOL] "strand" representation + free label

Tina, That would be very difficult to do at present...I'll take this as a suggestion for a future version. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -

RE: [PyMOL] electrostatic potential ramp

If I understand the question correctly, the answer is disable ramp-name Cheers, Warren > Hello: > > Is there anyway to remove the colour ramp from an electrostatic potential > figure via a script (help hide doesn't list anything reasonable for this > and there is nothing that I can see in the s

RE: [PyMOL] cartoons through nonstandard residues

ersions of PyMOL should not suffer from this problem. alter all.type='ATOM' alter name P,name='P1' sort Thanks for your help in quashing that bug! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (

RE: [PyMOL] cartoons through nonstandard residues

David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type=’ATOM’ sort rebuild I’m thinking about disabling this behavior before the next release… Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

RE: [PyMOL] cartoons through nonstandard residues

David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type='ATOM' sort rebuild I'm thinking about disabling this behavior before the next release. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal S

RE: [PyMOL] comprehensive rules for selection-expressions

;elems CHNOS*" represent? I'd really appreciate more > comprehensive documentation. > That's just the coloring for Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur, in the color pop-up menu. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

[PyMOL] Upcoming Rendering Changes. Comments?

or 4. Prior behavior can be restored by changing two settings (ray_oversample_cutoff->0 and antialias->0 or 2). If you have strong objections to these changes, please speak up. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scie

RE: [PyMOL] ray trace stereo

need higher-quality images with a higher resolution, then provide an explicit width and height to ray: set antialias,1 ray 2000,1500,angle=-3 png image1.png ray 2000,1500,angle=3 png image2.png Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] installing 0.90 from scratch

Richard, "layer0/MemoryCache.c", needs to be added to the source list in setup.py. Sorry for the inconvenience... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650

RE: [PyMOL] command list in Mac OSX

Milton, To get a complete list of commands, hit TAB on a blank command line. My apologies that PyMOL isn't more obvious, but thanks for the reminder -- I'm working on making life easier! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D.

RE: [PyMOL] H-bond display

Gareth, cmd.identify returns the input indexing, which will correspond to the PDB file. cmd.index returns the internal indexing, which will correspond to cmd.get_model help identify help index Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D

RE: [PyMOL] H-bond display

Gareth, CGO is currently the way to go... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourcefor

RE: [PyMOL] mesh question

. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforg

RE: [PyMOL] Nuvision stereo glasses?

mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Dr. Dan

RE: [PyMOL] appending states to objects

the beginning of the animation. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users

RE: [PyMOL] weird artifact with cylindrical helices

oblem. Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.

RE: [PyMOL] map line width

war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax   (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dennis Wolan Sent: Tuesday, July 15, 2003 10

RE: [PyMOL] PyMOL tutorial

epresents the official (but not infallible) doctrine. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...

RE: [PyMOL] how to get minimum distances in script?

pend((x,y,z))") result_list.append(( ((stored.qry_info), (stored.qry_xyz)), map(None,stored.nbr_info, stored.nbr_xyz))) # the rest of the task is just pure Python math, using the # values stored in result_list. for a in result_list: print "Query:",a[0] if len(a

[PyMOL] 0.90 Two Minor Bug Advisories

nder CVS. Cheers, Warren PS. Today I also added support for InsightII's ascii/formatted grid file (just in case anyone has some old Biosym GRD files lying around...). -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] loops-to-cylinders connectivity

pick" first to make sure no atom is currently picked). hide ribbon I'll see what we can do about this in the future... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] Interaction surfaces

future version...) -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Be

RE: [PyMOL] CGOs, where to start?

Felix, > I've read over the manual, and I think I understand the principle behind a > CGO. What I would like to do is generate a wall-&-floor type background > for an animation I'm putting together. I've followed the example given by > David Cooper (http://ginsberg.med.virginia.edu/~dcoop/Help/

[PyMOL] New Map Formats Coming...

mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] ca trace

Jason, In version 0.90, there is a ribbon_trace setting which allows you to do this for the ribbon representation. In versions 0.91+, I've added the same thing for cartoons "cartoon_trace". Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano,

RE: [PyMOL] Electrostatic potential maps in PyMOL

65x65 for testing purposes? Please include the associated PDB file for visual verification. Thanks! Looks like we'll need to push out another release sooner rather than later... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scienti

RE: [PyMOL] Electrostatic potential maps in PyMOL

with any effective way of doing it without risking a floating exception on finicky hardware. Any ideas? If we can just determine the "enddian-ness" of the incoming file, then the rest is a snap. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal S

RE: [PyMOL] pymol on OSX

John, The "native" OSX port is incomplete with respect to the user interface. You can get the complete package if you use the Fink version under X11. PyMOL doesn't export 3D data well at present. Cheers, Warren -- mailto:war...@delanoscientific.com Warren

RE: [PyMOL] Further functionality

> 1- calculation of surface potentials- will this be coming soon? Creation of a Possion-Boltzman solver is a bit of work, so this will not happen very soon -- probably not until we accumulate enough sponsorship to contract with someone to perform the task. But perhaps someone might volunteer to w

[PyMOL] RE: (no subject)

> I just download PYMOL into my Linux and it's working very nicely but I > want to check > whether it is possible to move a pdb file within a 3D density map > independently to get a > best fitting. Yes, you can move the molecule, but not the map. First, get into editing mode: edit_mode (or se

RE: [PyMOL] can't initialize module sglite

odules directory. I hope this helps. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net

RE: [PyMOL] stereo parameters?

1 or 2. For hardware or cross-eye, set stereo_shift, 4 For walleye, set stereo_angle, 1.95 set stereo_shift, 4 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax

RE: [PyMOL] element colouring schemes

To define a new color, use the set_color command: set_color my_color,[0.5,0.5,1.0] color my_color, all Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message-

[PyMOL] PyMOL v0.90 Released

e 0.90 Fink update in order to get menus... -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] Missing cmyk.png

Sorry Ulrich, The file got left off verson 0.88 - will be in 0.90, which will be released this week. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original

RE: [PyMOL] Bonds

Tsjerk, Not currently. The closest you can achieve is to write out the PDB file, delete the object, and then read it back in. - Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] Re: PyMOL-users digest, Vol 1 #346 - 14 msgs

David, Try turning off "roving_origin" set roving_origin,0 Also, I think the zooming only happens in orthoscopic mode -- I may be able to get rid of that side-effect. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

RE: [PyMOL] pymol crashes with large pdb files

That's likely the problem. If you need to reduce RAM consumption during raytracing (at the cost of performance), try reducing hash_max to 80 or 60. set hash_max,60 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] extracting number of residues

:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Cameron M

RE: [PyMOL] Partnership Negotiations

Whoops - I meant to delete that message, must have spaced out and hit the accept button. Sorry for (accidentally) propagating spam. DeLano Scientific does not endorse "Chief Mgbe" or his ilk...these are all scams. Any email with the words "Nigeria" "bank" and "million" should be moved straight

RE: [PyMOL] show model

Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] O

RE: [PyMOL] default atomic radii

Scott, Currently they are hard-coded in the C, but can be changed after loading the molecule using: alter selection, vdw=number for example: alter elem c, vdw=1.8 alter elem n, vdw=1.4 alter elem h, vdw=1.1 etc. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano

RE: [PyMOL] Missing parts

Jason, The command zoom complete=1 Will guarantee that no parts of the molecule get clipped Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- >

RE: [PyMOL] color schemes

Kaushik, set auto_color,off before opening the first file. or util.cbag afterwards. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Mess

RE: [PyMOL] Problem with session saving using PyMOL 0.88 under OSX

p was a success. Not a Home Run, but a solid Double! PPS. Luca, if you have a ".pml" file which can reproduce your session save problem, please email it to me -- Thanks. -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1

[PyMOL] PyMOL v0.89 for Win32 Released! (a v0.88 Bug Fix)

ow, non-Windows platforms are unaffected by the 0.88 bug, but I'll issue another release soon just in case. "pymol-0_89-bin-win32.zip" is the file you want: http://sourceforge.net/project/showfiles.php?group_id=4546 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeL

[PyMOL] DeLano Scientific Offline Until Thurs 6/12/2003

PyMOLers, I am hitting the road to pay a PyMOL-focused visit to one of the world's top pharmaceutical companies. Let's hope they like what they see! DeLano Scientific support will be back online as of Thursday, June 12th. Cheers, Warren -- mailto:war...@delanoscientific.com Warren

RE: [PyMOL] color by grasp phi map potential?

...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Seth Harris > Sent: Satur

RE: [PyMOL] command line usage of pymol?

Sure pymol -c script-name or python-program-name or pdb-file, etc. For example: pymol -qc load.pml movie.pml render.py "-c" disables the GUI and "-q" suppresses the startup output. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Princi

RE: [PyMOL] Stereo introduction?

t work. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourc

RE: [PyMOL] C-alpha trace

Martin, hide show ribbon set ribbon_sampling,1 And if your model only contains CA atoms, you'll also need to issue: set ribbon_trace,1 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650

RE: [PyMOL] RE: [ccp4bb]: Pymol stereo question (fwd)

4) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Be

[PyMOL] Roving Density Tips

See the manual page for details: http://pymol.sourceforge.net/newman/user/S0200start.html#5_4_3 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Thomas Earnest [mai

[PyMOL] RE: [ccp4bb]: Pymol stereo question

Rotating by a small angle is the best it can currently do unless you send the geometries to an outside rendering package, such as PovRay. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593

[PyMOL] RE: [ccp4bb]: Pymol stereo question

PyMOL, and then assemble them outside of PyMOL. We'll make this foolproof in a future version. Cheers, Dr. PyMOL -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: o

[PyMOL] RE: PyMOL manual

t as another reasonable way that we might get to a reasonable state of documentation for PyMOL -- in fact I'd prefer it. But if that doesn't happen, then we'll eventually get there anyway via economic incentives and my own stubborn efforts. Cheers, Warren -- mailto:war...@delanos

RE: [PyMOL] CGOs and TRIANGLE primitive

this release...perhaps in the next version -- I'll need to in order to make cartoons transparent, which is a planned enhancement. For now, you're probably out of luck, unless you call OpenGL Directly via PyOpenGL. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. D

[PyMOL] PyMOL v0.88 Released

it through your sponsorship. Let's continue to work together in a global partnership to help PyMOL reach its full potential! Please buy a license and maintenance subscription if you can afford to do so. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] settings for Adobe Premiere

#x27;re presenting off of your laptop and not sending files over the internet. For files posted on the internet, JP's comments are right on the money -- "late model" codecs are a must. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal Scientist DeLano

RE: [PyMOL] Labels

dation is to do exactly what Scott suggests -- drop labels in afterwards using PowerPoint, Illustrator, or Photoshop. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- Fr

RE: [PyMOL] Changing lines to be dashed lines

... show sticks set stick_radius, 0.1 etc. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ow...@lists.sourceforge.net [mailto:pymol-users-ow

RE: [PyMOL] plane2colour

r...@delanoscientific.com Warren L. DeLano Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message----- From: Warren L. DeLano [mailto:war...@delanoscientific.com] Sent: Tuesday, May 27, 2003 1:17 PM To: 'Warren L. DeLano'; 'Björn Kau

RE: [PyMOL] mpng command

Jason, The "mpng" command in recent versions of PyMOL takes two arguments, first and last, which control which frames are rendered. You can have your script set these appropriately based on where the job is running. Cheers, Warren -- mailto:war...@delanoscientific.com Warren

RE: [PyMOL] plane2colour

users-ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano Sent: Tuesday, May 27, 2003 9:19 AM To: 'Björn Kauppi'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] plane2colour Bjorn, Good news, I just recently added opaque, colored, "insides" of cartoons, sur

RE: [PyMOL] plane2colour

Bjorn, Good news, I just recently added opaque, colored, "insides" of cartoons, surfaces, and spheres to the upcoming release. In version 0.88 and beyond, "set interior_color, color-name" will achieve this effect. Cheers, Warren -- mailto:war...@delanoscientific.

RE: [PyMOL] PyMOL compatibility w/ NVidia card on rh9 system

...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Cameron Mura Sent: Wednesday, May 21, 2003 12:50

RE: [PyMOL] select buried water molecules

olor("red",a[1]) # now show interior... clip slab,10 # end of script Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:p

RE: [PyMOL] Callsbacks to mouse event

en done. Sorry. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Mahesh

RE: [PyMOL] how to show sticks for the side-chains of selected residues

Yibin, show sticks, (not name c,n,o) show cartoon set cartoon_smooth_loops, 0 and perhaps set cartoon_flat_sheets, 0 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message

RE: [PyMOL] Atom Ordering when Saving

t;%c + a[11:] c = c + 1 ll.append(a) g=open("reorder.pdb","w") g.write(string.join(ll,'')) g.close() Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Origin

RE: [PyMOL] Packaging PyMol as part of another application on Windows

). I hope this helps! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Beha

RE: [PyMOL] residues in alternate conformations as ribbon

should be possible to create the appearance of a single object. Hope this helps! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax   (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net

RE: [PyMOL] connect atoms

...@delanoscientific.com Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax   (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Florian Schmitzberger Sent: Tuesday, May 13, 2003 1:42 AM

RE: [PyMOL] pkfrag

-- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Thursday, May

RE: [PyMOL] helix thickness and diameter

Florian, There's two "b" s in dumbbell. cartoon_dumbbell_length etc. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From:

RE: [PyMOL] Question on Mutagenesis

utton. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Ra

RE: [PyMOL] surface

Molecular (a discrete approximation to the Connolly surface). -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad

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